Abstract Organisms have evolved a number of molecular surveillance pathways to monitor and prevent cellular damage. One such system is the nonsense mediated decay (NMD) pathway. NMD functions to detect mRNAs with premature termination codons, such as occur in many inherited diseases, and target these mRNAs for rapid degradation and prevent the generation of truncated mutant proteins. However, NMD can exacerbate the effects of many inherited mutations: by targeting and degrading transcripts that otherwise would encode proteins with sufficient biochemical activity for normal function, the NMD pathway can essentially cause a complete loss of activity, and a subsequent disease. Thus inhibition of NMD has potential therapeutic benefit. However, NMD is an essential process in higher animals, including mammals, indicating the NMD pathway has important functions in normal cell biology. These functions are not well understood. Therefore, while NMD-inhibition therapies hold promise for treating certain genetic diseases, realizing this potential will require understanding the biological roles of NMD. To address this important question, we are using Drosophila to study the requirements for NMD during normal development and physiology. Specifically, we plan to determine whether NMD function is required in all tissues for organismal viability and identify the key targets mediating the biological roles of the NMD pathway in critical tissues. We are also using Drosophila to identify the cis-acting signals and trans-acting protein machinery that mediate NMD. We will identify cis-acting sequences directing endogenous targets for NMD-mediated degradation by combining microarray analysis of Drosophila NMD mutants with detailed bioinformatic analysis. To identify trans-acting components, we will use the genetic tools available in Drosophila to conduct efficient, large-scale genetic screens directed at identifying mutations that affect NMD. The screens are designed to identify novel components of the pathway, including those required for organismal viability. The screens will also identify new mutations in known NMD components, which will help define the molecular interactions among these components. Since the NMD pathway is conserved throughout evolution it is likely that the knowledge gained from these approaches will be applicable across a broad range of organisms, including humans. Project Narrative The nonsense mediated decay (NMD) pathway is a cellular system that controls the activity level of genes by altering the amount of gene products made. Mutations which lead to inherited diseases also cause the mutated genes to be regulated by NMD. In the fruit fly Drosophila many genes are also regulated by NMD, providing a model to understand the NMD process in detail.